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Detailed information for vg0717056384:

Variant ID: vg0717056384 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 17056384
Reference Allele: AAlternative Allele: G
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.89, A: 0.12, others allele: 0.00, population size: 218. )

Flanking Sequence (100 bp) in Reference Genome:


TACCCAGAATAGTGAAGCCCCAATTCCATAGTACCTTTCAGATAGCGCATTACTCGCTCAAGCACACGCCAGTGATCATCTCCCGGATTAGAGGTAAACC[A/G]
GCTCAACTTGCTCAGAGCAAAGGAGATATCAGGCCTAGTTGCACTAGCCAGGTACATCAGCGAGCCAATGATTTGGGAGTATTCCAATTGATTCCTAACA

Reverse complement sequence

TGTTAGGAATCAATTGGAATACTCCCAAATCATTGGCTCGCTGATGTACCTGGCTAGTGCAACTAGGCCTGATATCTCCTTTGCTCTGAGCAAGTTGAGC[T/C]
GGTTTACCTCTAATCCGGGAGATGATCACTGGCGTGTGCTTGAGCGAGTAATGCGCTATCTGAAAGGTACTATGGAATTGGGGCTTCACTATTCTGGGTA

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 64.70% 35.00% 0.32% 0.00% NA
All Indica  2759 95.00% 4.70% 0.25% 0.00% NA
All Japonica  1512 10.80% 89.20% 0.00% 0.00% NA
Aus  269 84.80% 12.30% 2.97% 0.00% NA
Indica I  595 97.50% 1.70% 0.84% 0.00% NA
Indica II  465 96.30% 3.70% 0.00% 0.00% NA
Indica III  913 96.90% 3.00% 0.11% 0.00% NA
Indica Intermediate  786 90.10% 9.80% 0.13% 0.00% NA
Temperate Japonica  767 15.00% 85.00% 0.00% 0.00% NA
Tropical Japonica  504 5.60% 94.40% 0.00% 0.00% NA
Japonica Intermediate  241 8.30% 91.70% 0.00% 0.00% NA
VI/Aromatic  96 4.20% 95.80% 0.00% 0.00% NA
Intermediate  90 45.60% 54.40% 0.00% 0.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0717056384 A -> G LOC_Os07g29110.1 downstream_gene_variant ; 2689.0bp to feature; MODIFIER silent_mutation Average:46.103; most accessible tissue: Minghui63 flag leaf, score: 68.16 N N N N
vg0717056384 A -> G LOC_Os07g29110-LOC_Os07g29140 intergenic_region ; MODIFIER silent_mutation Average:46.103; most accessible tissue: Minghui63 flag leaf, score: 68.16 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0717056384 1.34E-06 3.85E-09 mr1265_2 Ind_All YES Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0717056384 NA 7.37E-13 mr1325_2 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0717056384 NA 7.87E-14 mr1326_2 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0717056384 2.28E-06 2.29E-06 mr1514_2 Jap_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0717056384 5.92E-07 3.76E-09 mr1528_2 Ind_All YES Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0717056384 NA 2.58E-08 mr1690_2 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251